Through bioactivity-guided chemical analysis of Selaginella lepidophylla, biflavonoids robustaflavone (1), 2,3-dihydrorobustaflavone (2), and 2,3-dihydrorobustaflavone-5-methyl ether (3) were isolated and their structures confirmed by spectroscopic and spectrometric analyses. Their NMR resonances were unambiguously assigned from HMBC, NOESY, and NOESY-1D experiments, and absolute configurations of 2 and 3 were established. Compound 3 has not been reported, and although structure of 2 was described before, the 13C NMR assignment does not correlate with the structure reported. Therefore, this is the first report of 2. All compounds inhibited ATP production. Compounds 1 and 2 behaved as Hill reaction inhibitors. 1 interacted with photosystem II, transforming the reaction centers to silent centers at 300 and 600 μM. The interaction and inhibition target of 2 was located on Cyt b6f to PC. The three compounds also behaved as energy transfer inhibitors, 3 being the most active.